Start simple: QC, trim adapters, mapping, methylation calling and identification of differentially methylated regions.
Use standard tools in the field: FastQC+other custom quality metrics (QC), trimgalore (adapter trimming), bismark (mapping + meth calling), BSmooth or something else for DMR identification.
Start simple: QC, trim adapters, mapping, methylation calling and identification of differentially methylated regions.
Use standard tools in the field: FastQC+other custom quality metrics (QC), trimgalore (adapter trimming), bismark (mapping + meth calling), BSmooth or something else for DMR identification.